Sequence
atgc intronic sequence ATGC exonic sequencegtaggcatattgcagtgtcattttgcatttatccagactatatatgtattggtgatctttgatttggtggctttcagGTACGGGGAATTGAAACAGTGACTACTTATGACCCAACAACTGAAGAGTTTGTGATAAATACTCCTTGTGAATCTGCTCAGAAGTATTGGATCGGTGAGG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G06310.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G06310.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os06g24704.1 (Oryza sativa), 3'ss of exon 2
------------------gtaggcatattgcagtgtcattttgc-atttatccagactatatatgtattggtgatctttgatttggtggctttcagGTACGGGGAATTGAAACAGTGACTACTTATGACCCAACAACTGAAGAGTTTGTGATAAATACTCCTTGTGAATCTGCTCAGAAGTATTGGATCGGTGAGG
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gtatgtgatgatattttggtcaaattactgaattgtagttttgttagctgtgttgatgagatttttctttgccttatttgact----aatttgaagGTCCGAGGAATTGAGACAGTGGCTACTTATGATATTAAAACAAGAGAGTTTGTGATAAATACTCCTTGTGAATCAGCCCAGAAGTACTGGATTGGTGGAG
upper sequence: AT1G06310.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G014136_T01 (Zea mays), 3'ss of exon 2
-----------------------gtaggcatattgcagtgtcattttgcatttatccagactatatatgtattggtgatctttgatttggtggctttcagGTACGGGGAATTGAAACAGTGACTACTTATGACCCAACAACTGAAGAGTTTGTGATAAATACTCCTTGTGAATCTGCTCAGAAGTATTGGATCGGTGAGG
| | | | || | || | || | | || | || || || || || | ||| |||| | |||| || ||||| |||||| | | |||||||| || ||| |||||| | ||||||||||| |||||||| ||||||||||| ||||| |||| |
gtacgtgcatagatttgggctaagcatactttttacggtataatctcac---taactgtgctgattaagttctgttgctgtttc-tttgtta--caaaagGTGCGAGGAATAGAAACAATAGCAACTTATGATTCAGAAACAAGAGAGTTCATCATAAATACTCCATGTGAATCAGCTCAGAAGTACTGGATTGGTGGAG
upper sequence: AT1G06310.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA12G14060.1 (Glycine max), 3'ss of exon 2
----------------------gtaggcatattgcagtgtcattttg--catt-tatccagactatatatgtattggtgatctttgatttggtggctttc--agGTACGGGGAATTGAAACAGTGACTACTTATGACCCAACAACTGAAGAGTTTGTGATAAATACTCCTTGTGAATCTGCTCAGAAGTATTGGATCGGTGAGG
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gtatgtgaaggttgcccaataagttgggtcattaggtctacatgtaaattattatgcttttgccttgtcacttttaataatcctttccagactaattttcatagGTTCGAGGAATTGAAACAGTCACTACTTATGATTCAAACACCGGGGAATTTGTCATCAATACTCCATGTGAATCGGGTCAGAAGTATTGGATTGGTGGTG
upper sequence: AT1G06310.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA06G43840.1 (Glycine max), 3'ss of exon 2
----------------------gtaggcatattgcagtgtcattttgcatttatccag-----actatatatgtattggtgatctttgatttggtggctttca--gGTACGGGGAATTGAAACAGTGACTACTTATGACCCAACAACTGAAGAGTTTGTGATAAATACTCCTTGTGAATCTGCTCAGAAGTATTGGATCGGTGAGG
|| || | | ||| || | | |||| | | | | | || | ||| | | ||||| ||| || |||||||||||||| ||||||||||| ||| || | ||| ||||| || ||||| || |||||||| | ||||||||||||||| |||| |
gtatgtgaaggttgctcaataagttggggtcat-tagttccacatgtaaattattatgcttttgccttgtcacttttaataatcccttccagactaattttcatagGTTCGAGGAATTGAAACAGTCACTACTTATGATTCAAACACCGGAGAATTTGTCATCAATACCCCATGTGAATCGGGTCAGAAGTATTGGATTGGTGGTG
upper sequence: AT1G06310.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv12s0028g02660.t01 (Vitis vinifera), 3'ss of exon 2
----------------------------gtaggcatattgcagtgtcattttgcatttatccagactatatatgtattggtgatctttgatttggtggctt-tcagGTACGGGGAATTGAAACAGTGACTACTTATGACCCAACAACTGAAGAGTTTGTGATAAATACTCCTTGTGAATCTGCTCAGAAGTATTGGATCGGTGAGG
| || | || || || | || || | | || || || ||| || | |||||| || || ||||||||||| || || |||||| ||| ||||| ||||||||| || || | ||| |||||||| ||||||||||| ||||| || | |
gtatgtgaaggttgtttgatcatttggttttgggccaccaggcctgtatgatgatgttcttcattctccctgttgtttagttttcattggttctttcatgggtcagGTTCGAGGTATTGAAACAGTTACCACATATGACTCAAAAACTGGAGAGTTTGTTATTAACAGTCCCTGTGAATCAGCTCAGAAGTACTGGATAGGAGGAG
upper sequence: AT1G06310.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S149_61V6.1 (Physcomitrella patens), 3'ss of exon 2
-------------------------------------------------------------------------------------------------------gtaggcatattgcagtgtcattttgcatttatccagactatatatgtattg----gtgatctttgatt-tggtggctttc-----agGTACGGGGAATTGAAACAGTGACTACTTATGACCCAACAACTGAAGAGTTTGTGATAAATACTCCTTGTGAATCTGCTCAGAAGTATTGGATCGGTGAGG
| | || | || | ||| | | || | | || ||| ||| || | | ||| |||| |||| || || ||||||||||||||||||||||| | | || || ||||| | || |||||||||||||||||||||| ||||| ||||| || | |
gtaagtgttggaatttcctaaggtcttttttgttgtctcaaaactgattggtatgaagctgaaactaattctaattgataggtgtcaattaatctttagaaccgatagtttactacacgattgtttgattgtaggctttccttttagcatcgtgaaaagtggtctcagaatatagtgattttctgatcagGTGCGAGGCATTGAAACAGTGACTACTTATGATACTTCCACAGAGGAGTTCATCATCGATACTCCTTGTGAATCTGCTCAAAAGTACTGGATTGGAGGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgcatttatccagactatatatgtattggtgatctttgatttggtggctttcagGTACGGGGAATTGAAACAGTGACTACTTATGACCCAACAACTGAAGAGTTTGTGATAAATACTCCTTGTGAATCTGCTCAGAAGTATTGGATCGGTGAGG
ctttgat putative branch site (score: 5)
ctttc putative PPT
actatatatgtatt TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaggcatattgcagtgtcattttgcatttatccagactatatatgtattggtgatctttgatttggtggctttcagGTACGGGGAATTGAAACAGTGACTACTTATGACCCAACAACTGAAGAGTTTGTGATAAATACTCCTTGTGAATCTGCTCAGAAGTATTGGATCGGTGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT